diff options
Diffstat (limited to 'web/webqtl/management')
| -rwxr-xr-x | web/webqtl/management/GenoUpdate.py | 1279 | ||||
| -rwxr-xr-x | web/webqtl/management/__init__.py | 0 | ||||
| -rwxr-xr-x | web/webqtl/management/assignUserToDatasetPage.py | 159 | ||||
| -rwxr-xr-x | web/webqtl/management/createUserAccountPage.py | 161 | ||||
| -rwxr-xr-x | web/webqtl/management/deletePhenotypeTraitPage.py | 196 | ||||
| -rwxr-xr-x | web/webqtl/management/editHeaderFooter.py | 200 | ||||
| -rwxr-xr-x | web/webqtl/management/exportPhenotypeDatasetPage.py | 228 | ||||
| -rwxr-xr-x | web/webqtl/management/managerMainPage.py | 130 |
8 files changed, 0 insertions, 2353 deletions
diff --git a/web/webqtl/management/GenoUpdate.py b/web/webqtl/management/GenoUpdate.py deleted file mode 100755 index 6ee87dec..00000000 --- a/web/webqtl/management/GenoUpdate.py +++ /dev/null @@ -1,1279 +0,0 @@ -""" -Maintainnce module. Update Genotype data, user can update the Marker -one by one through web interface, or batch update one Population -through submit genotype file -""" - -import string -import os - -from htmlgen import HTMLgen2 as HT - -from base.templatePage import templatePage -from base import webqtlConfig -from utility import webqtlUtil -from dbFunction import webqtlDatabaseFunction - - - -""" -The Fields of Geno, GenoXRef table that be shown to user for updating -""" -MarkerSpeciesInfoField = ['Name', 'Chr', 'Mb', 'Sequence', 'Source'] -MarkerGroupInfoField = ['cM', 'Used_for_mapping'] -MarkerInfoField = MarkerSpeciesInfoField + MarkerGroupInfoField -markerName_Feild_Separator = '_and_' - - -# retrieve all of the Inbred Set names and group them by Species -def retrieveSpeciesInbredSetGroup(cursor): - """ - @type cursor: MySQLdb.connect.cursor - rtype: dictionary - return: dictionary, the key are the name of Species, the value are - the InbredSet Names that related with the Species - """ - - SpeciesInbredSet={} - cursor.execute(""" - SELECT - Species.Id, Species.Name - FROM - Species, InbredSet - WHERE - Species.Id=InbredSet.SpeciesId AND - MappingMethodId = 1 - GROUP BY - Species.Id - """) - species=cursor.fetchall() - - for item in species: - SpeciesId, SpeciesName = item - cursor.execute("SELECT distinct(InbredSet.Name) FROM InbredSet, GenoFreeze, GenoXRef WHERE SpeciesId=%d and GenoFreeze.InbredSetId = InbredSet.Id and GenoXRef.GenoFreezeId = GenoFreeze.Id and GenoXRef.Used_for_mapping='Y' " % SpeciesId) - InbredSetNames=cursor.fetchall() - - InbredSetNameList=[] - for InbredSetName in InbredSetNames: - if InbredSetName[0]=='BXD300': - continue - InbredSetNameList.append(InbredSetName[0]) - SpeciesInbredSet[SpeciesName]=InbredSetNameList - - return SpeciesInbredSet - - -#XZ: This function will be called in many places. -# Each caller might organize the result in different way. -# So the raw database results are returned. -def retrieveGenoCode(cursor, InbredSetName): - - cursor.execute(""" - SELECT - AlleleType, AlleleSymbol, DatabaseValue - FROM - GenoCode, InbredSet - WHERE - InbredSet.Name = '%s' AND - InbredSetId = InbredSet.Id - """ % InbredSetName ) - results = cursor.fetchall() - - GenoCode = [] - - for one_result in results: - GenoCode.append(one_result) - - return GenoCode - - -def retrieveGeneticTypeOfInbredSet(cursor, InbredSetName): - - GeneticType = '' - - cursor.execute(""" - SELECT - GeneticType - FROM - InbredSet - WHERE - InbredSet.Name=%s - """, InbredSetName) - result=cursor.fetchone() - - if result: - GeneticType = result[0] - - return GeneticType - - - - -#XZ: For one group, retrieve the list of all strains that are in StrainXRef and used for mapping -def retrieveStrainUsedForMapping(cursor, GroupName): - """ - @type cursor: MySQLdb.connect.cursor - @type GroupName: string - @param GroupName: In MySQL table, it's called Inbred Set name, in GeneNetwork's Homepage, it's called group - - @rtype: list - @return: The Strain's names that related with the Inbred Set - """ - - cursor.execute(""" - SELECT - Strain.Name - FROM - Strain, StrainXRef, InbredSet - WHERE - InbredSet.Name = '%s' AND - StrainXRef.InbredSetId=InbredSet.Id AND - StrainXRef.StrainId = Strain.Id AND - StrainXRef.Used_for_mapping = 'Y' - ORDER BY - StrainXRef.OrderId - """ % GroupName) - results = cursor.fetchall() - - StrainList=[] - for item in results: - StrainList.append(item[0]) - - return StrainList - - -#XZ: For one group, retrieve the dictionary of all strain id, name pairs that are in StrainXRef and used for mapping -def retrieveStrainNameIdUsedForMapping(cursor, GroupName): - """ - @type cursor: MySQLdb.connect.cursor - @type GroupName: string - @param GroupName: In MySQL table, it's called Inbred Set name, in GeneNetwork's Homepage, it's called group - - @rtype: dictionary - @return: dictionary, the key is Strain's name, the value is Strain's Id - """ - - StrainNameId = {} - - cursor.execute(""" - SELECT - Strain.Name, Strain.Id - FROM - Strain, StrainXRef, InbredSet - WHERE - InbredSet.Name = '%s' AND - StrainXRef.InbredSetId=InbredSet.Id AND - StrainXRef.StrainId = Strain.Id AND - StrainXRef.Used_for_mapping = 'Y' - ORDER BY - StrainXRef.OrderId - """ % GroupName) - results = cursor.fetchall() - - for item in results: - StrainNameId[item[0]] = item[1] - - return StrainNameId - - - -# retrieve the strain's id by name, the Strain should bind with Inbred Set -#if the strain's name cann't be found, the id will be set to 'None' -def retrieveStrainIds(cursor, StrainList, InbredSetName): - """ - @type cursor: MySQLdb.connect.cursor - @type StrainList: list - @param StrainList: the list of Strains' Name - @type InbredSetName: string - - @rtype: dictionary - @return: dictionary, the key is Strain's name, the value is Strain's Id - """ - - StrainIds={} - for Strain in StrainList: - cursor.execute(""" - SELECT - Strain.Id - FROM - Strain,StrainXRef,InbredSet - WHERE - Strain.Id=StrainXRef.StrainId AND - StrainXRef.InbredSetId=InbredSet.Id AND - Strain.Name=%s AND - InbredSet.Name=%s - """, (Strain, InbredSetName)) - result=cursor.fetchone() - if result: - StrainIds[Strain]=result[0] - else: - StrainIds[Strain]=None - - return StrainIds - - - -# retrieve the GenoFreezeId -def retrieveGenoFreezeId(cursor, InbredSetName): - """ - @type cursor: MySQLdb.connect.cursor - @type InbredSetName: string - - @rtype: int - @return: the GenoFreezeId related with the Inbred Set's name - """ - - cursor.execute(""" - SELECT - GenoFreeze.Id - FROM - InbredSet, GenoFreeze - WHERE - GenoFreeze.InbredSetId=InbredSet.Id AND - InbredSet.Name=%s - """, InbredSetName) - result=cursor.fetchone() - - if result: - return result[0] - else: - return None - - -# retrieve the DataId -def retrieveDataId(cursor, GenoId, InbredSetName): - """ - @type cursor: MySQLdb.connect.cursor - @type GenoId: int - @type InbredSetName: int - - @rtype: int - @return: the DataId relate with the Geno(Marker) and the Inbred Set - """ - - cursor.execute(""" - SELECT - GenoXRef.DataId - FROM - GenoXRef, GenoFreeze, InbredSet - WHERE - GenoXRef.GenoFreezeId=GenoFreeze.Id AND - GenoFreeze.InbredSetId=InbredSet.Id AND - GenoXRef.GenoId=%s AND - InbredSet.Name=%s - """, (GenoId, InbredSetName)) - result=cursor.fetchone() - - if result: - return result[0] - else: - return None - - -# retrieve the max Id from GenoData table -def retrieveMaxGenoDataId(cursor): - """ - @type cursor: MySQLdb.connect.cursor - - @rtype: int - @return: the maximal Id of the Data table - """ - - cursor.execute('SELECT max(Id) FROM GenoData') - results = cursor.fetchone() - - return results[0] - - -# retrieve the max Id from Geno table -def retrieveMaxGenoId(cursor): - """ - @type cursor: MySQLdb.connect.cursor - - @rtype: int - @return: the maximal Id of the Geno table - """ - - cursor.execute('SELECT max(Id) FROM Geno') - results = cursor.fetchone() - - return results[0] - - -# retrieve the strain names related with a data.Id -# Note that for one group, even if one strain is labelled as Used_for_mapping in StrainXRef table, -# if the allele value for this strain is unknown, there is no record for this strain along with this group in GenoData table. -# So the list of strains returned by this function <= list of strains returned by function retrieveStrainUsedForMapping. -def retrieveDataStrains(cursor, DataId): - """ - @type cursor: MySQLdb.connect.cursor - @type DataId: int - - @rtype: list - @return: the names list of the Strains that related with the DataId - """ - - cursor.execute("SELECT Strain.Name FROM Strain, GenoData WHERE GenoData.StrainId=Strain.Id AND GenoData.Id=%s", DataId) - results=cursor.fetchall() - - Strains=[] - for item in results: - Strains.append(item[0]) - - return Strains - - - -def retrieveMarkerNameForGroupByRange(cursor, InbredSetName, Chr, MbStart, MbEnd): - - MarkerName = [] - - SpeciesId = webqtlDatabaseFunction.retrieveSpeciesId(cursor, InbredSetName) - - GenoFreezeId = retrieveGenoFreezeId(cursor, InbredSetName) - - MbStartClause = '' - MbEndClause = '' - - try: - MbStartClause = 'and Mb >= %s ' % float(MbStart) - except: - pass - - try: - MbEndClause = 'and Mb <= %s' % float(MbEnd) - except: - pass - - - cmd = "SELECT Geno.Name FROM Geno, GenoXRef WHERE Geno.SpeciesId=%s and Chr='%s' " % (SpeciesId, Chr) + MbStartClause + MbEndClause + " and GenoXRef.GenoFreezeId=%s and GenoXRef.GenoId=Geno.Id and GenoXRef.Used_for_mapping='Y' order by Mb" % (GenoFreezeId) - - cursor.execute(cmd) - - results = cursor.fetchall() - for one_result in results: - MarkerName.append( one_result[0] ) - - return MarkerName - - - -# retrive the Marker's infomation from Geno and GenoXRef table, -# the information includes the Id of the marker matchs and all of the MarkerInfoField that defined upper -def retrieveMarkerInfoForGroup(cursor, MarkerName, InbredSetName): - """ - @type cursor: MySQLdb.connect.cursor - @type MarkerName: string - - @rtype: list - @return: the Marker's Id, Name, Chr, cM, Mb, Sequence, Source - """ - - - SpeciesId = webqtlDatabaseFunction.retrieveSpeciesId(cursor, InbredSetName) - - GenoFreezeId = retrieveGenoFreezeId(cursor, InbredSetName) - - cmd = ','.join( MarkerInfoField ) - cmd = "SELECT Geno.Id," + cmd + " FROM Geno, GenoXRef WHERE Geno.SpeciesId=%s and Geno.Name='%s' and GenoXRef.GenoFreezeId=%s and GenoXRef.GenoId=Geno.Id" % (SpeciesId, MarkerName, GenoFreezeId) - cursor.execute(cmd) - result = cursor.fetchone() - - if result: - return result - else: - return None - - -def retrieveMarkerPositionForSpecies(cursor, GenoId): - - Chr = '' - Mb = '' - - cursor.execute( "select Chr, Mb from Geno where Id=%s" % GenoId ) - result = cursor.fetchone() - - Chr = result[0] - Mb = result[1] - - return Chr, Mb - - -def checkIfMarkerInSpecies (cursor, MarkerName, InbredSetName): - - cmd = "SELECT Geno.Id FROM Geno, InbredSet, Species WHERE Geno.SpeciesId=Species.Id AND Geno.Name='%s' and InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (MarkerName, InbredSetName) - cursor.execute(cmd) - result = cursor.fetchone() - - if result: - return result - else: - return None - - - - -# retrive the Marker's Used_for_mapping status from MySQL -# for one marker, if we want it be contains in the special genotype file, we can set its value in Used_for_mapping column to 'Y' in the GenoXRef table. -# In GenoXRef table, the default value of column Used_for_mapping is 'N'. -# GenoXRef table is the relationship of the Marker and the allele value that this marker in special genotype -def mappingForThisGroup(cursor, GenoFreezeId, GenoId): - """ - @type cursor: MySQLdb.connect.cursor - @type MarkerName: string - @type InbredSetName: string - - @rtype: boolean - @return: the status that if the marker's exprssion value in special Inbred Set will be hide(not shown in genotype file) - """ - - cursor.execute(""" - SELECT - Used_for_mapping - FROM - GenoXRef - WHERE - GenoFreezeId = %s AND - GenoId = %s - """, (GenoFreezeId, GenoId)) - result = cursor.fetchone() - - Used_for_mapping = False - if result: - if result[0] == 'Y': - Used_for_mapping = True - - return Used_for_mapping - - -# Retrieve the allele values of a Marker in specific genotype -# -# 1. Retrieve strain name and allele value from GenoData table -# 2. Put the result into dictionary, the key is strain name. The value is allele (-1, 0, 1). -# -# Note even one strain is used for mapping for one group in GenoXRef table. When its genotype is unknown, -# it has no record in GenoData table (e.g., BXD102 strain for marker rs6376963). -# In this case, the dictionary key doesn't include this strain. -def retrieveAllele (cursor, GenoFreezeId, GenoId): - """ - @type cursor: MySQLdb.connect.cursor - @type MarkerName: string - @type InbredSetName: string - - @rtype: dictionary - @return: dictionary, the keys are strain names, the values are alleles - that the Marker in specials Inbred Set - """ - - Alleles = {} - - #retrieve the strains' name and their allele values - cursor.execute(""" - SELECT - Strain.Name, GenoData.Value - FROM - Strain, GenoData, GenoXRef - WHERE - GenoXRef.GenoFreezeId=%s AND - GenoXRef.GenoId=%s AND - GenoXRef.DataId=GenoData.Id AND - GenoData.StrainId=Strain.Id - """, (GenoFreezeId, GenoId)) - results = cursor.fetchall() - - # set the allele value of the strain that appears in Data to the value from Data - for item in results: - Alleles[item[0]]=item[1] - - return Alleles - - - -def retrieveGroupNeedExported (cursor, GenoId): - - Groups = [] - - cursor.execute(""" - SELECT - InbredSet.Name - FROM - InbredSet, GenoFreeze, GenoXRef - WHERE - Used_for_mapping = 'Y' AND - GenoXRef.GenoId = %s AND - GenoXRef.GenoFreezeId = GenoFreeze.Id AND - GenoFreeze.InbredSetId = InbredSet.Id - """, (GenoId) ) - results = cursor.fetchall() - - if results: - for one_result in results: - Groups.append( one_result[0] ) - - return Groups - - -def get_chr_num (cursor, Chr='', SpeciesId=0): - - chr_num = 99 - - cmd = "SELECT OrderId FROM Chr_Length WHERE Name='%s' and SpeciesId=%s " % (Chr, SpeciesId) - - cursor.execute(cmd) - result = cursor.fetchone() - - if result: - chr_num = result[0] - - return chr_num - - - -def addGeno(cursor, GenoId, InbredSetName, MarkerWebID, fd): - - SpeciesId = webqtlDatabaseFunction.retrieveSpeciesId(cursor, InbredSetName) - - Name = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Name' ) - Chr = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Chr' ) - Mb = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Mb' ) - Sequence = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Sequence' ) - Source = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Source' ) - - chr_num = get_chr_num (cursor, Chr, SpeciesId) - - cmd = "INSERT INTO Geno (Id, SpeciesId, Name, Marker_Name, Chr, Mb, Sequence, Source, chr_num) VALUES (%s, %s, '%s', '%s', '%s', %s, '%s', '%s', %s )" % (GenoId, SpeciesId, Name, Name, Chr, Mb, Sequence, Source, chr_num) - cursor.execute(cmd) - - - -def updateGeno(cursor, GenoId, InbredSetName, MarkerWebID, fd): - - SpeciesId = webqtlDatabaseFunction.retrieveSpeciesId(cursor, InbredSetName) - - Chr = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Chr' ) - cmd = "UPDATE Geno SET Chr='%s' WHERE Id=%s" % (Chr, GenoId) - cursor.execute(cmd) - - chr_num = get_chr_num (cursor, Chr, SpeciesId) - cmd = "UPDATE Geno SET chr_num=%s WHERE Id=%s" % (chr_num, GenoId) - cursor.execute(cmd) - - Mb = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Mb' ) - cmd = "UPDATE Geno SET Mb=%s WHERE Id=%s" % (Mb, GenoId) - cursor.execute(cmd) - - Sequence = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Sequence' ) - cmd = "UPDATE Geno SET Sequence='%s' WHERE Id=%s" % (Sequence, GenoId) - cursor.execute(cmd) - - Source = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Source' ) - cmd = "UPDATE Geno SET Source='%s' WHERE Id=%s" % (Source, GenoId) - cursor.execute(cmd) - - -def updateGenoXRef(cursor, GenoFreezeId, GenoId, MarkerWebID, fd): - - cM = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'cM' ) - cmd = "UPDATE GenoXRef SET cM=%s WHERE GenoFreezeId=%s AND GenoId=%s" % (cM, GenoFreezeId, GenoId) - cursor.execute(cmd) - - Used_for_mapping = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Used_for_mapping') - - if Used_for_mapping == 'on': - cmd = "UPDATE GenoXRef SET Used_for_mapping='Y' WHERE GenoFreezeId=%s AND GenoId=%s" % (GenoFreezeId, GenoId) - else: - cmd = "UPDATE GenoXRef SET Used_for_mapping='N' WHERE GenoFreezeId=%s AND GenoId=%s" % (GenoFreezeId, GenoId) - cursor.execute(cmd) - - - -def addGenoXRef(cursor, GenoFreezeId, GenoId, DataId, MarkerWebID, fd): - - cM = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'cM') - - Used_for_mapping = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Used_for_mapping') - - Used_for_mapping_db_value = 'N' - if Used_for_mapping == 'on': - Used_for_mapping_db_value = 'Y' - - cmd = "INSERT INTO GenoXRef (GenoFreezeId, GenoId, DataId, cM, Used_for_mapping) VALUES (%s, %s, %s, %s, '%s')" % (GenoFreezeId, GenoId, DataId, cM, Used_for_mapping_db_value) - - cursor.execute(cmd) - - - -def insertGenoData(cursor, InbredSetName, DataId, MarkerWebID, fd): - - StrainList = retrieveStrainUsedForMapping (cursor, InbredSetName) - StrainIds = retrieveStrainIds(cursor, StrainList, InbredSetName) - - for Strain in StrainList: - if fd.formdata.has_key( MarkerWebID + markerName_Feild_Separator + Strain ): - value = fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + Strain ) - - # XZ: The legitimate values are hard coded. Should be dynamical (from database). - try: - int_value = int(float(value)) - - if int_value in (0, 1, -1): - cmd = "INSERT INTO GenoData VALUES(%d,%d,%s)"%(DataId, StrainIds[Strain], int_value) - cursor.execute(cmd) - except: - pass - - -#XZ: This function is to compare the input position (Chr, Mb) with position in database. -# It should be executed before update database record. -def getAllGroupsNeedExported(cursor, GroupNeedExport=[], GenoId=0, Chr='', Mb=''): - - db_Chr, db_Mb = retrieveMarkerPositionForSpecies(cursor, GenoId) - - if str(Chr) == str(db_Chr) and str(Mb) == str(db_Mb): - pass - else: - temp = retrieveGroupNeedExported (cursor, GenoId) - for one_group in temp: - try: - GroupNeedExport.index(one_group) - except: - GroupNeedExport.append(one_group) - - return GroupNeedExport - - - - -class GenoUpdate(templatePage): - - def __init__(self, fd): - - templatePage.__init__(self, fd) - - # get mysql connection, if not, show error - if not self.openMysql(): - heading = "Geno Updating" - detail = ["Can't connect to MySQL server"] - self.error(heading=heading,detail=detail) - return - - - self.dict['title'] = 'Geno Updating' - - # status is the switch, direct what's the next step - try: - status = fd.formdata.getvalue('status') - except: - status = '' - - if fd.formdata.getvalue('submit')=='Clear': - status='' - - if not status: # show - self.dict['body']=self.showSelectionPage() - elif status=='search' or status == 'addNewMarker': - InbredSetName = fd.formdata.getvalue('InbredSetName') - Chr = fd.formdata.getvalue('Chr') - - if not InbredSetName: - self.dict['body']= "Please select the population." - return - elif not Chr: - self.dict['body']= "Please input Chr." - return - else: - self.dict['body']=self.showAllMarkers (InbredSetName, Chr, fd) - - elif status == 'editMarkerTable': - self.dict['body'] = self.editMarkerTable(fd) - - elif status == 'checkMarkerHasBeenInGroup': # check if there is anything changed. - InbredSetName = fd.formdata.getvalue('InbredSetName') - Marker = fd.formdata.getvalue('Name') - self.dict['body'] = self.checkMarkerHasBeenInGroup (InbredSetName, Marker, fd) - - elif status=='changeMarker': #insert new marker - InbredSetName = fd.formdata.getvalue('InbredSetName') - self.dict['body']=self.changeMarker(InbredSetName, fd) - - else: #this part is used to test, the proceduce won't come here in normal cycle - HTTable = HT.TableLite(border=0, cellspacing=1, cellpadding=1,align="center") - for key in fd.formdata.keys(): - HTTable.append(HT.TR(HT.TD(key), HT.TD(':'), HT.TD(fd.formdata.getvalue(key)))) - self.dict['body'] = HTTable - - - - - # this is the first page, user upload their genotype file here, or input - # which marker they want to update - def showSelectionPage(self): - """ - The first page, in this page, user can upload a genotype file for batch updating, - or enter a Marker for one by one updating - - @rtype: string - @return: HTML - """ - - # get the InbredSet Name list - SpeciesInbredSet = retrieveSpeciesInbredSetGroup(self.cursor) - - # generate homepage - - HTTableLite_Population = HT.TableLite(border=0, width="100%") - - HTTD_InbredSet = HT.TD(width="30%") - - HTSelect_InbredSetNames = HT.Select(name='InbredSetName') - HTSelect_InbredSetNames.append("") - for SpeciesName in SpeciesInbredSet.keys(): - HT_OptGroup_Species=HT.Optgroup() - HT_OptGroup_Species.label=SpeciesName - for InbredSetName in SpeciesInbredSet[SpeciesName]: - HT_OptGroup_Species.append(InbredSetName) - HTSelect_InbredSetNames.append(HT_OptGroup_Species) - - HTTD_InbredSet.append( HT.Font(HT.Strong('Group (required) '), color="red") ) - HTTD_InbredSet.append(HTSelect_InbredSetNames) - - HTTableLite_Population.append(HT.TR(HTTD_InbredSet)) - - HTTableLite_Marker = HT.TableLite(border=0, width="100%") - HTTD_Chr = HT.TD() - HTTD_Chr.append( HT.Font(HT.Strong('Chr (required) '), color="red") ) - HTTD_Chr.append(HT.Input(name='Chr', size=3)) - HTTD_Mb = HT.TD() - HTTD_Mb.append(HT.Font(HT.Strong('Mb')), ' from ') - HTTD_Mb.append(HT.Input(name='MbStart', size=10)) - HTTD_Mb.append(' to ') - HTTD_Mb.append(HT.Input(name='MbEnd', size=10)) - HTTableLite_Marker.append(HT.TR(HTTD_Chr), HT.TR(), HT.TR(HTTD_Mb) ) - - - - HTTableLite_Search = HT.TableLite(border=1, width="100%") - HTTableLite_Search.append( - HT.TR(HT.TD(HTTableLite_Population, height="100")), - HT.TR(HT.TD("Enter Chr and Mb range", HT.BR(), HT.BR(), - HTTableLite_Marker, - height="100")) - ) - - - HTInput_Submit = HT.Input(type='submit', name='submit', value='Submit',Class="button") - HTInput_Clear = HT.Input(type='submit', name='submit', value='Clear', Class="button") - HTInput_FormId = HT.Input(type='hidden', name='FormID', value='updGeno') - HTInput_Status = HT.Input(type='hidden', name='status', value='search') - - HTForm_Search = HT.Form(cgi=os.path.join(webqtlConfig.CGIDIR, 'main.py'), \ - enctype= 'multipart/form-data', submit='') - HTForm_Search.append(HTTableLite_Search) - HTForm_Search.append(HTInput_Submit) - HTForm_Search.append(HTInput_Clear) - - HTForm_Search.append(HTInput_FormId) - HTForm_Search.append(HTInput_Status) - - HTTableLite_Content = HT.TableLite(border=1, width="100%") - HTTableLite_Content.append(HT.TR(HT.TD(HTForm_Search, width="50%"), \ - HT.TD(HT.Font(HT.Strong("Instructions:"), HT.BR(),HT.BR(), "The \"from\" and \"to\" inputs for Mb range are optional.", HT.BR(),HT.BR(), "If only the \"from\" input is provided, the result will be all markers from the input position to the end of chromosome.", HT.BR(),HT.BR(), "If only the \"to\" input is provided, the result will be all markers from the beginning of the chromosome to the input position.", HT.BR(),HT.BR(), "If no input is provided for Mb range, the result will be all markers on the chromosome."), valign='top', width="50%") \ - )) - - return HTTableLite_Content - - - - - def searchMappingMarkerInDB (self, InbredSetName="", Chr='', MbStart='', MbEnd=''): - """ - Show Marker's information for updating or inserting - - @type InbredSetName: string - @type MarkerName: string - - @rtype: string - @return: The HTML form that contains the Marker's information - """ - - - MarkerInfoDic = {} - - MarkerNamesByRange = retrieveMarkerNameForGroupByRange(self.cursor, InbredSetName, Chr, MbStart, MbEnd) - - for one_MarkerName in MarkerNamesByRange: - one_MarkerGroupInfo = retrieveMarkerInfoForGroup (self.cursor, one_MarkerName, InbredSetName) - MarkerInfoDic[ one_MarkerName ] = one_MarkerGroupInfo - - return MarkerNamesByRange, MarkerInfoDic - - - - def showAllMarkers( self, InbredSetName, Chr, fd ): - - MbStart = fd.formdata.getvalue('MbStart') - MbEnd = fd.formdata.getvalue('MbEnd') - - inputStatus = fd.formdata.getvalue('status') - - newMarkerNameQuantityDic = {} - MarkerNameAdded = [] - - MarkerNames, MarkerInfoDic = self.searchMappingMarkerInDB (InbredSetName=InbredSetName, Chr=Chr, MbStart=MbStart, MbEnd=MbEnd) - - MainTable = HT.TableLite(border=1, cellspacing=1, cellpadding=1,align="left") - - if inputStatus == 'search': - - - InputTable = HT.TableLite(border=1, cellspacing=1, cellpadding=1,align="left") - - InputTable.append( HT.TR( HT.TD( HT.Textarea(name="InputNewMarker", rows=10, cols=20)), - HT.TD(HT.Font( "Add one input per line.", HT.BR(), HT.BR(), \ - "Each input must be in the format of: existing marker name,quantity", HT.BR(), HT.BR(), \ - "For instance, the input rs6376963, 2 will add two markers after rs6376963", HT.BR(), HT.BR(), \ - "The input existing marker name must have been shown in the table below.", HT.BR(), HT.BR(), color="red"), \ - HT.Input(type='submit', name='inputmarker_submit', value='Add new markers', Class="button", onClick= "changeStatusSubmit(this.form, 'addNewMarker');" ) ) ) ) - - MainTable.append( HT.TR(HT.TD(InputTable)) ) - else: - InputNewMarkerString = fd.formdata.getvalue('InputNewMarker') - - InputNewMarkerLines = InputNewMarkerString.split('\n') - for one_line in InputNewMarkerLines: - one_line = one_line.strip() - if len(one_line) > 0: - one_line_tokens = one_line.split(',') - try: - first_token = one_line_tokens[0].strip() - second_token = one_line_tokens[1].strip() - second_token = int( second_token ) - if first_token in MarkerNames: - newMarkerNameQuantityDic[ first_token ] = second_token - except: - pass - - - MarkerTable = HT.TableLite(border=1, cellspacing=1, cellpadding=1,align="left") - - HeaderRow = HT.TR() - - - for one_field in MarkerSpeciesInfoField: - HeaderRow.append( HT.TD(one_field) ) - - for one_field in MarkerGroupInfoField: - HeaderRow.append( HT.TD(one_field) ) - - GenoFreezeId = retrieveGenoFreezeId(self.cursor, InbredSetName) - StrainList = retrieveStrainUsedForMapping (self.cursor, InbredSetName) - - for one_strain in StrainList: - HeaderRow.append( HT.TD(one_strain) ) - - MarkerTable.append( HeaderRow ) - - - for one_MarkerName in MarkerNames: - one_MarkerGroupInfo = MarkerInfoDic[ one_MarkerName ] - oneMarkerRow = self.showOneMarker (InbredSetName=InbredSetName, MarkerName=one_MarkerName, suffix="", MarkerGroupInfo=one_MarkerGroupInfo, StrainList=StrainList, marker_type='existed') - MarkerTable.append( oneMarkerRow ) - - if newMarkerNameQuantityDic.has_key(one_MarkerName): - for i in range(0, newMarkerNameQuantityDic[one_MarkerName]): - MarkerNameAdded.append( one_MarkerName + '_add_' + str(i) ) - oneMarkerRow = self.showOneMarker (InbredSetName=InbredSetName, MarkerName=one_MarkerName, suffix='_add_' + str(i), MarkerGroupInfo=one_MarkerGroupInfo, StrainList=StrainList, marker_type='add') - MarkerTable.append( oneMarkerRow ) - - - - MarkerTable.append( HT.TR(HT.TD( HT.Input(type='submit', name='markertable_submit', value='Edit marker table',Class="button", onClick= "changeStatusSubmit(this.form, 'editMarkerTable');") )) ) - - MainTable.append( HT.TR(HT.TD(MarkerTable)) ) - - - HTInput_Submit = HT.Input(type='hidden', name='submit', value='Submit',Class="button") - HTInput_FormId = HT.Input(type='hidden', name='FormID', value='updGeno') - HTInput_Status = HT.Input(type='hidden', name='status', value='') - HTInput_InbredSetName = HT.Input(type='hidden', name='InbredSetName', value=InbredSetName) - HTInput_Chr = HT.Input(type='hidden', name='Chr', value=Chr) - HTInput_MbStart = HT.Input(type='hidden', name='MbStart', value=MbStart) - HTInput_MbEnd = HT.Input(type='hidden', name='MbEnd', value=MbEnd) - HTInput_MarkerNamesExisted = HT.Input(type='hidden', name='MarkerNamesExisted', value=','.join(MarkerNames) ) - HTInput_MarkerNamesAdded = HT.Input(type='hidden', name='MarkerNamesAdded', value=','.join(MarkerNameAdded) ) - - - HTForm_showAllMarkers = HT.Form(cgi=os.path.join(webqtlConfig.CGIDIR, 'main.py'), enctype= 'multipart/form-data', submit=HTInput_Submit) - - HTForm_showAllMarkers.append( MainTable ) - HTForm_showAllMarkers.append(HTInput_FormId) - HTForm_showAllMarkers.append(HTInput_Status) - HTForm_showAllMarkers.append(HTInput_InbredSetName) - HTForm_showAllMarkers.append(HTInput_Chr) - HTForm_showAllMarkers.append(HTInput_MbStart) - HTForm_showAllMarkers.append(HTInput_MbEnd) - HTForm_showAllMarkers.append(HTInput_MarkerNamesExisted) - HTForm_showAllMarkers.append(HTInput_MarkerNamesAdded) - - return HTForm_showAllMarkers - - - - def showOneMarker (self, InbredSetName="", MarkerName="", suffix="", MarkerGroupInfo=[], StrainList=[], marker_type=''): - - GenoInfo={} - - #XZ: The first item of MarkerInfo is Geno.Id - GenoId = MarkerGroupInfo[0] - - for i in range(1, len(MarkerGroupInfo)): - if MarkerGroupInfo[i] != None: - GenoInfo[ MarkerInfoField[i-1] ] = str(MarkerGroupInfo[i]) - else: - GenoInfo[ MarkerInfoField[i-1] ] = '' - - if GenoInfo['Used_for_mapping'] == 'Y': - GenoInfo['Used_for_mapping'] = True - else: - GenoInfo['Used_for_mapping'] = False - - - MarkerRow = HT.TR() - - # Species level info - for i in range(0, len(MarkerSpeciesInfoField)): - if MarkerSpeciesInfoField[i] == 'Name': - if marker_type == 'existed': - MarkerRow.append( HT.TD(GenoInfo['Name']) ) - else: - MarkerRow.append(HT.TD(HT.Input(name = MarkerName + suffix + markerName_Feild_Separator + MarkerSpeciesInfoField[i], size=20, maxlength=500, value=MarkerName + suffix ))) - else: - MarkerRow.append(HT.TD(HT.Input(name = MarkerName + suffix + markerName_Feild_Separator + MarkerSpeciesInfoField[i], size=10, maxlength=500, value=GenoInfo[MarkerSpeciesInfoField[i]]))) - - # Group level info - for i in range(0, len(MarkerGroupInfoField)): - if MarkerGroupInfoField[i] != 'Used_for_mapping': - MarkerRow.append( HT.TD(HT.Input(name = MarkerName + suffix + markerName_Feild_Separator + MarkerGroupInfoField[i], size=10, value=GenoInfo[MarkerGroupInfoField[i]]))) - else: - MarkerRow.append( HT.TD(HT.Input(type='checkbox', name= MarkerName + suffix + markerName_Feild_Separator + 'Used_for_mapping', checked=GenoInfo['Used_for_mapping'] ))) - - # retrive Marker allele values - GenoFreezeId = retrieveGenoFreezeId(self.cursor, InbredSetName) - Alleles = retrieveAllele (self.cursor, GenoFreezeId, GenoId) - - for i in range(0, len(StrainList)): - try: - Value = Alleles[StrainList[i]] - except: - Value = 'X' # 'X' is the symbol for unknown allele - MarkerRow.append( HT.TD(HT.Input(name = MarkerName + suffix + markerName_Feild_Separator + StrainList[i], size=3, maxlength=5, value=Value))) - - - return MarkerRow - - - def editMarkerTable (self, fd): - - InbredSetName = fd.formdata.getvalue('InbredSetName') - Chr = fd.formdata.getvalue('Chr') - - MbStart = fd.formdata.getvalue('MbStart') - MbEnd = fd.formdata.getvalue('MbEnd') - - MarkerNamesExistedString = fd.formdata.getvalue('MarkerNamesExisted') - MarkerNamesAddedString = fd.formdata.getvalue('MarkerNamesAdded') - - MarkerNamesExisted = [] - MarkerNamesAdded = [] - - MarkerNamesExistedString = MarkerNamesExistedString.strip() - MarkerNamesExisted = MarkerNamesExistedString.split(',') - - MarkerNamesAddedString = MarkerNamesAddedString.strip() - if MarkerNamesAddedString: - MarkerNamesAdded = MarkerNamesAddedString.split(',') - - GroupNeedExport = [] - # To simplify the business logic, just add this group to the list anyway - GroupNeedExport.append(InbredSetName) - - - for one_marker in MarkerNamesExisted: - if self.checkMarkerHasBeenInGroup(InbredSetName=InbredSetName, MarkerName=one_marker, fd=fd): - GroupNeedExport = self.changeMarker( InbredSetName=InbredSetName, MarkerWebID=one_marker, MarkerName=one_marker, GroupNeedExport=GroupNeedExport, fd=fd) - - if MarkerNamesAdded: - for one_marker in MarkerNamesAdded: - input_name = fd.formdata.getvalue( one_marker + markerName_Feild_Separator + 'Name' ) - GroupNeedExport = self.changeMarker( InbredSetName=InbredSetName, MarkerWebID=one_marker, MarkerName=input_name, GroupNeedExport=GroupNeedExport, fd=fd) - - export_info = self.exportAllGenoFiles( GroupNeedExport ) - - contents = [] - - contents.append(export_info) - - HTInput_FormId = HT.Input(type='hidden', name='FormID', value='updGeno') - HTInput_Back = HT.Input(type="submit", name="backButton", value="Back to main page", Class="button") - HTForm_Back = HT.Form(name='StrainForm', cgi=os.path.join(webqtlConfig.CGIDIR, 'main.py'), \ - enctype= 'multipart/form-data', submit=HTInput_Back) - HTForm_Back.append(HTInput_FormId) - - contents.append(str(HTForm_Back)) - - return '<BR>'.join(contents) - - # return "%s" % export_info - - - - def checkMarkerHasBeenInGroup(self, InbredSetName="", MarkerName="", fd=None): - - isChanged = False - - # retrive Marker information from database - MarkerGroupInfo = retrieveMarkerInfoForGroup (self.cursor, MarkerName, InbredSetName) - - GenoId = MarkerGroupInfo[0] - - GenoInfo={} - - for i in range(1, len(MarkerGroupInfo)): - if MarkerGroupInfo[i] != None: - GenoInfo[MarkerInfoField[i-1]] = str( MarkerGroupInfo[i] ) - else: - GenoInfo[MarkerInfoField[i-1]] = '' - - if GenoInfo['Used_for_mapping'] == 'Y': - GenoInfo['Used_for_mapping'] = True - else: - GenoInfo['Used_for_mapping'] = False - - - # check the changing of Geno information - - for i in range(0, len(MarkerInfoField)): - - if MarkerInfoField[i] == 'Name': - continue - - webInputValue = fd.formdata.getvalue( MarkerName + markerName_Feild_Separator + MarkerInfoField[i] ) - - - if MarkerInfoField[i] == 'Used_for_mapping': - if webInputValue == 'on': - webInputValue = True - else: - webInputValue = False - - - if GenoInfo[MarkerInfoField[i]] != webInputValue: - isChanged = True - - # retrive Marker alleles - GenoFreezeId = retrieveGenoFreezeId(self.cursor, InbredSetName) - db_alleles = retrieveAllele (self.cursor, GenoFreezeId, GenoId) - StrainList = retrieveStrainUsedForMapping (self.cursor, InbredSetName) - - - # check the changing of allele values - - for i in range(0, len(StrainList)): - webInputValue = fd.formdata.getvalue(MarkerName + markerName_Feild_Separator + StrainList[i]) - - if not db_alleles.has_key(StrainList[i]): - #XZ: This is hard coded. - #XZ: The best way is to check if the input value is in ('B', 'D', 'H'). - if webInputValue.upper() != 'X': # 'X' is the symbol for unknown allele. - isChanged = True - else: - if str( db_alleles[StrainList[i]]) != webInputValue: - isChanged = True - - - return isChanged - - - def changeMarker(self,InbredSetName="", MarkerWebID="", MarkerName="", GroupNeedExport=[], fd=None): - - GenoFreezeId = retrieveGenoFreezeId( self.cursor, InbredSetName ) - - MarkerGroupInfo = retrieveMarkerInfoForGroup(self.cursor, MarkerName, InbredSetName) - - # This marker has record for this group. - # Need to keep the original GeneId and marker name. - if MarkerGroupInfo: - - #XZ: The first item of MarkerInfo is Geno.Id - GenoId = MarkerGroupInfo[0] - - #This function should be excuted before update Chr and Mb in database. - GroupNeedExport = getAllGroupsNeedExported(self.cursor, GroupNeedExport=GroupNeedExport, GenoId=GenoId, \ - Chr=fd.formdata.getvalue(MarkerWebID + markerName_Feild_Separator + 'Chr'), \ - Mb=fd.formdata.getvalue(MarkerWebID + markerName_Feild_Separator + 'Mb') ) - - # Update the info in Geno (Chr, Mb, Sequence, Source). - updateGeno(self.cursor, GenoId, InbredSetName, MarkerWebID, fd) - - # Update GenoXRef (cM, Used_for_mapping) - updateGenoXRef(self.cursor, GenoFreezeId, GenoId, MarkerWebID, fd) - - # Keep the original GenoXRef.DataId value. - DataId = retrieveDataId(self.cursor, GenoId, InbredSetName) - - # Delete the original alleles - cmd = "delete from GenoData where Id=%s" % DataId - self.cursor.execute(cmd) - - # Insert new alleles. - insertGenoData(cursor=self.cursor, InbredSetName=InbredSetName, DataId=DataId, MarkerWebID=MarkerWebID, fd=fd) - - else: # No record for this group. - - hasInfoForSpecies = checkIfMarkerInSpecies(self.cursor, MarkerName, InbredSetName) - - if hasInfoForSpecies: - - # Keep the original GenoId. - GenoId = hasInfoForSpecies[0] - - #This function should be excuted before update Chr and Mb in database. - GroupNeedExport = getAllGroupsNeedExported(self.cursor, GroupNeedExport=GroupNeedExport, GenoId=GenoId, \ - Chr=fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Chr' ), \ - Mb=fd.formdata.getvalue( MarkerWebID + markerName_Feild_Separator + 'Mb') ) - - - # Update the info in Geno (Chr, Mb, Sequence, Source). - updateGeno(self.cursor, GenoId, InbredSetName, MarkerWebID, fd) - - - # Get new GenoData.Id - DataId = retrieveMaxGenoDataId(self.cursor) + 1 - - # Add record in GenoXRef table for this group. - addGenoXRef(self.cursor, GenoFreezeId, GenoId, DataId, MarkerWebID, fd) - - # Add record in GenoData table. - insertGenoData(cursor=self.cursor, InbredSetName=InbredSetName, DataId=DataId, MarkerWebID=MarkerWebID, fd=fd) - - else: - # Get new Geno.Id - GenoId = retrieveMaxGenoId(cursor=self.cursor) + 1 - - # Add record in Geno - addGeno(self.cursor, GenoId, InbredSetName, MarkerWebID, fd) - - # Get new GenoData.Id - DataId = retrieveMaxGenoDataId(self.cursor) + 1 - - # Add record into GenoXRef table. - addGenoXRef(self.cursor, GenoFreezeId, GenoId, DataId, MarkerWebID, fd) - - #Add record into GenoData table. - insertGenoData(cursor=self.cursor, InbredSetName=InbredSetName, DataId=DataId, MarkerWebID=MarkerWebID, fd=fd) - - return GroupNeedExport - - - - def exportAllGenoFiles (self, InbredSetNameList = []): - - warning = "As to the change made, the following groups need to be exported to generate new geno files: %s\n<br><br> " % str(InbredSetNameList) - - whiteList = ['BXD'] - - warning = warning + "At current development stage, the following groups can be exported to generate geno files: %s\n<br><br>" % str(whiteList) - warning = warning + "Here are the geno files that are ACTUALLY exported according to the change you made:\n<br>" - - blackList = [] - for one_group in InbredSetNameList: - if one_group in whiteList: - self.exportOneGenoFile( one_group ) - warning = warning + "<a href='/genotypes/%s.geno" % one_group + "'>" + one_group + " geno file</a>\n<br>" - else: - blackList.append(one_group) - - return warning - - - - def exportOneGenoFile (self, InbredSetName=''): - - geno_file = open(webqtlConfig.GENODIR + InbredSetName + '.geno', 'w') - - query = "select SpeciesId from InbredSet where Name='%s' " % InbredSetName - self.cursor.execute( query ) - SpeciesId = self.cursor.fetchone()[0] - - GenoFreezeId = retrieveGenoFreezeId( self.cursor, InbredSetName ) - - StrainUsedForMapping = retrieveStrainUsedForMapping(self.cursor, InbredSetName ) - - StrainNameIdUsedForMapping = retrieveStrainNameIdUsedForMapping( self.cursor, InbredSetName ) - - GenoCode_record = retrieveGenoCode(self.cursor, InbredSetName ) - - Allle_value_symbol = {} - symbol_for_unknown = '' - - for one_result in GenoCode_record: - if str(one_result[2]) != 'None': - Allle_value_symbol[one_result[2]] = one_result[1] - else: - symbol_for_unknown = one_result[1] - - - geno_file.write('@name:%s\n' % InbredSetName ) - - GeneticType = retrieveGeneticTypeOfInbredSet(self.cursor, InbredSetName ) - - geno_file.write('@type:%s\n' % str(GeneticType) ) - - for one_result in GenoCode_record: - geno_file.write('@%s:%s\n' % (one_result[0], one_result[1]) ) - - geno_file.write('Chr\tLocus\tcM\tMb') - - for one_strain in StrainUsedForMapping: - geno_file.write('\t%s' % one_strain ) - - - query = "select Geno.Chr, Geno.Name, GenoXRef.cM, Geno.Mb, GenoXRef.DataId from Geno, GenoXRef where SpeciesId=%s and GenoFreezeId=%s and Used_for_mapping='Y' and Geno.Id=GenoId order by chr_num, Mb" % (SpeciesId, GenoFreezeId) - self.cursor.execute( query ) - results = self.cursor.fetchall() - - StrainId_Allele = {} - - for one_result in results: - Chr, Name, cM, Mb, DataId = one_result - geno_file.write('\n%s\t%s\t%s\t%s' % (Chr, Name, cM, Mb) ) - - StrainId_Allele = {} - - query = "select StrainId, value from GenoData where Id=%s " % DataId - self.cursor.execute( query ) - GenoData_results = self.cursor.fetchall() - - for one_GenoData_result in GenoData_results: - StrainId_Allele[ one_GenoData_result[0] ] = one_GenoData_result[1] - - for one_strain_name in StrainUsedForMapping: - one_strain_id = StrainNameIdUsedForMapping[ one_strain_name ] - - if StrainId_Allele.has_key( one_strain_id ): - one_allele_value = StrainId_Allele[one_strain_id] - one_allele_symbol = Allle_value_symbol[ one_allele_value ] - geno_file.write( '\t%s' % one_allele_symbol ) - else: - geno_file.write( '\t%s' % symbol_for_unknown ) - - - - - - - - - - - diff --git a/web/webqtl/management/__init__.py b/web/webqtl/management/__init__.py deleted file mode 100755 index e69de29b..00000000 --- a/web/webqtl/management/__init__.py +++ /dev/null diff --git a/web/webqtl/management/assignUserToDatasetPage.py b/web/webqtl/management/assignUserToDatasetPage.py deleted file mode 100755 index 8e089526..00000000 --- a/web/webqtl/management/assignUserToDatasetPage.py +++ /dev/null @@ -1,159 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -import os -import string - -from htmlgen import HTMLgen2 as HT - -from base.templatePage import templatePage -from base import webqtlConfig - -#XZ, 02/06/2009: Xiaodong created this class -class assignUserToDatasetPage(templatePage): - - def __init__(self, fd): - - templatePage.__init__(self, fd) - - if not self.openMysql(): - return - - - ifVerified = fd.formdata.getvalue('ifVerified') - - if ifVerified != 'GN@UTHSC': - heading = "Error page" - detail = ["You are NoT verified as administrator."] - self.error(heading=heading,detail=detail) - return - else: - - ProbeSetFreeze_FullName = fd.formdata.getvalue('ProbeSetFreeze_FullName') - User_name = fd.formdata.getvalue('User_name') - - if ProbeSetFreeze_FullName and User_name: - ProbeSetFreeze_FullName = string.strip(ProbeSetFreeze_FullName) - User_name = string.strip(User_name) - - #XZ, check if the input dataset name exists. - self.cursor.execute( 'select count(FullName) from ProbeSetFreeze where FullName="%s"' % ProbeSetFreeze_FullName ) - result = self.cursor.fetchone() - if result: - row_count = result[0] - if row_count: - pass - else: - heading = "Error page" - detail = ["The dataset name %s does NOT exist in database." % ProbeSetFreeze_FullName] - self.error(heading=heading,detail=detail) - return - else: - heading = "Error page" - detail = ["No sql result returned when check dataset name."] - self.error(heading=heading,detail=detail) - return - - #XZ, check if the input user name exists. - self.cursor.execute( 'select count(name) from User where name="%s"' % User_name ) - result = self.cursor.fetchone() - if result: - row_count = result[0] - if row_count: - pass - else: - heading = "Error page" - detail = ["The user name %s does NOT exist in database." % User_name] - self.error(heading=heading,detail=detail) - return - else: - heading = "Error page" - detail = ["No sql result returned when check user name."] - self.error(heading=heading,detail=detail) - return - - self.cursor.execute( 'select AuthorisedUsers from ProbeSetFreeze where FullName="%s"' % ProbeSetFreeze_FullName ) - result = self.cursor.fetchone() # The FullName is unique. - if result: - AuthorisedUsers = result[0] - if not AuthorisedUsers: - self.cursor.execute('update ProbeSetFreeze set AuthorisedUsers="%s" where FullName="%s"' %(User_name, ProbeSetFreeze_FullName) ) - else: - AuthorisedUsersList=AuthorisedUsers.split(',') - if not AuthorisedUsersList.__contains__(User_name): - AuthorisedUsers = AuthorisedUsers + ',%s' % User_name - self.cursor.execute('update ProbeSetFreeze set AuthorisedUsers="%s" where FullName="%s"' %(AuthorisedUsers, ProbeSetFreeze_FullName) ) - else: - heading = "Error page" - detail = ["No sql result returned when query AuthorisedUsers."] - self.error(heading=heading,detail=detail) - return - - - TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee') - - dataHeading = HT.Paragraph('Confidential Dataset Table', Class="title") - - dataTable = HT.TableLite(border=1, cellpadding=0, cellspacing=0, Class="collap", width="100%") - - dataHeaderRow = HT.TR() - dataHeaderRow.append(HT.TD("Dataset Id", Class='fs14 fwb ffl b1 cw cbrb')) - dataHeaderRow.append(HT.TD("Dataset Full Name", Class='fs14 fwb ffl b1 cw cbrb')) - dataHeaderRow.append(HT.TD("Authorised User", Class='fs14 fwb ffl b1 cw cbrb')) - dataTable.append(dataHeaderRow) - - self.cursor.execute('select Id, FullName, AuthorisedUsers from ProbeSetFreeze where confidentiality=1 order by FullName,Id') - - result = self.cursor.fetchall() - - dataInfo = HT.Blockquote( 'There are %d confidential datasets.' % len(result) ) - - - for one_row in result: - ProbeSetFreeze_Id, ProbeSetFreeze_FullName, ProbeSetFreeze_AuthorisedUsers = one_row - dataRow = HT.TR() - dataRow.append(HT.TD("%s" % ProbeSetFreeze_Id, Class='fs12 fwn ffl b1 c222')) - dataRow.append(HT.TD("%s" % ProbeSetFreeze_FullName, Class='fs12 fwn ffl b1 c222')) - dataRow.append(HT.TD("%s" % ProbeSetFreeze_AuthorisedUsers, Class='fs12 fwn ffl b1 c222')) - dataTable.append(dataRow) - - assignUserForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='assignUserForm', submit=HT.Input(type='hidden')) - assignUserForm.append( - HT.Blockquote( - HT.Font('Dataset Full Name ', color='red'), - HT.Input(type='text' ,name='ProbeSetFreeze_FullName',value='', size=50,maxlength=200), - HT.Font(' User name ', color='red'), - HT.Input(type='text' ,name='User_name',value='', size=20,maxlength=20), - HT.Input(type='Submit', value='Submit', Class="button")), - HT.Input(type='hidden',name='FormID',value='assignUserToDataset'), - HT.Input(type='hidden',name='ifVerified',value='GN@UTHSC') - ) - - TD_LR.append(dataHeading, dataInfo, assignUserForm, dataTable, assignUserForm) - - self.dict['body'] = str(TD_LR) - self.dict['title'] = 'Confidential datasets' - diff --git a/web/webqtl/management/createUserAccountPage.py b/web/webqtl/management/createUserAccountPage.py deleted file mode 100755 index f002c6ed..00000000 --- a/web/webqtl/management/createUserAccountPage.py +++ /dev/null @@ -1,161 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -import os -import string - -from htmlgen import HTMLgen2 as HT - -from base.templatePage import templatePage -from base import webqtlConfig - - - -#XZ, 02/06/2009: Xiaodong created this class -class createUserAccountPage(templatePage): - - def __init__(self, fd): - - templatePage.__init__(self, fd) - - if not self.openMysql(): - return - - - ifVerified = fd.formdata.getvalue('ifVerified') - - if ifVerified != 'GN@UTHSC': - heading = "Error page" - detail = ["You are NoT verified as administrator."] - self.error(heading=heading,detail=detail) - return - else: - - user_name = fd.formdata.getvalue('user_name') - password = fd.formdata.getvalue('password') - retype_password = fd.formdata.getvalue('retype_password') - - if user_name or password or retype_password: - user_name = string.strip(user_name) - password = string.strip(password) - retype_password = string.strip(retype_password) - - #XZ, check if the input user name exists. - - if len(user_name) == 0: - heading = "Error page" - detail = ["The user name can NOT be empty."] - self.error(heading=heading,detail=detail) - return - - self.cursor.execute( 'select count(name) from User where name="%s"' % user_name ) - result = self.cursor.fetchone() - if result: - row_count = result[0] - if row_count: - heading = "Error page" - detail = ["The user name %s already exists in database. Please make up another user name." % user_name] - self.error(heading=heading,detail=detail) - return - else: - heading = "Error page" - detail = ["No sql result returned when check user name."] - self.error(heading=heading,detail=detail) - return - - # check password - if len(password) == 0 or len(retype_password) == 0: - heading = "Error page" - detail = ["The password can NOT be empty."] - self.error(heading=heading,detail=detail) - return - - if password != retype_password: - heading = "Error page" - detail = ["The passwords you entered are NOT consistent. Please go back and try again."] - self.error(heading=heading,detail=detail) - return - - #XZ, create new account - self.cursor.execute( "insert into User (name, password, createtime, privilege) values ('%s', SHA('%s'), Now(), 'user')" % (user_name, password) ) - - - #show user table. - TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee') - - userHeading = HT.Paragraph('User Table', Class="title") - - self.cursor.execute( 'select id, name, privilege from User order by name' ) - - result = self.cursor.fetchall() - - userInfo = HT.Blockquote( 'There are %d users.' % len(result) ) - - userTable = HT.TableLite(border=0, cellpadding=0, cellspacing=0, Class="collap", width="100%") - - userHeaderRow = HT.TR() - userHeaderRow.append(HT.TD("User Id", Class='fs14 fwb ffl b1 cw cbrb')) - userHeaderRow.append(HT.TD("User name", Class='fs14 fwb ffl b1 cw cbrb')) - userHeaderRow.append(HT.TD("User privilege", Class='fs14 fwb ffl b1 cw cbrb')) - userTable.append(userHeaderRow) - - for one_row in result: - User_Id, User_name, User_privilege = one_row - userRow = HT.TR() - userRow.append(HT.TD("%s" % User_Id, Class='fs12 fwn ffl b1 c222')) - userRow.append(HT.TD("%s" % User_name, Class='fs12 fwn ffl b1 c222')) - userRow.append(HT.TD("%s" % User_privilege, Class='fs12 fwn ffl b1 c222')) - userTable.append(userRow) - - #add user form - createUserAccountForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='createUserAccountForm', submit=HT.Input(type='hidden')) - - user_name = HT.Input(type='text' ,name='user_name',value='', size=20,maxlength=20) - password = HT.Input(type='password' ,name='password',value='', size=20,maxlength=20) - retype_password = HT.Input(type='password' ,name='retype_password',value='', size=20,maxlength=20) - submit_button = HT.Input(type='Submit', value='Submit', Class="button") - - createUserAccountForm.append( - HT.Blockquote( HT.Font('Create one new account: User Name ', color='red'), user_name, HT.Font(' Password ', color='red'), password, HT.Font(' Retype Password ', color='red'), retype_password, submit_button ), - HT.Input(type='hidden',name='FormID',value='createUserAccount'), - HT.Input(type='hidden',name='ifVerified',value='GN@UTHSC') - ) - - """ - #manager form - managerForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='managerForm', submit=HT.Input(type='hidden')) - managerForm.append( - HT.Input(type='Submit', value='Go to manager main page', Class="button"), - HT.Input(type='hidden',name='FormID',value='managerMain'), - HT.Input(type='hidden',name='ifVerified',value='GN@UTHSC') - ) - """ - - #TD_LR.append(managerForm, HT.BR(), userHeading, userInfo, HT.P(), createUserAccountForm, userTable, createUserAccountForm, HT.BR(), managerForm) - TD_LR.append(userHeading, userInfo, HT.P(), createUserAccountForm, userTable, createUserAccountForm) - - self.dict['body'] = str(TD_LR) - self.dict['title'] = 'User account' diff --git a/web/webqtl/management/deletePhenotypeTraitPage.py b/web/webqtl/management/deletePhenotypeTraitPage.py deleted file mode 100755 index de071003..00000000 --- a/web/webqtl/management/deletePhenotypeTraitPage.py +++ /dev/null @@ -1,196 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -import os - -from htmlgen import HTMLgen2 as HT - -from base.templatePage import templatePage -from base import webqtlConfig -from base.webqtlDataset import webqtlDataset -from base.webqtlTrait import webqtlTrait - - -#XZ, 09/07/2009: Xiaodong created this class -class deletePhenotypeTraitPage(templatePage): - - def __init__(self, fd): - - templatePage.__init__(self, fd) - - if not self.openMysql(): - return - - ifVerified = fd.formdata.getvalue('ifVerified') - status = fd.formdata.getvalue('status') - - if ifVerified != 'GN@UTHSC': - heading = "Error page" - detail = ["You are NoT verified as administrator."] - self.error(heading=heading,detail=detail) - return - else: - if status == 'input': - self.dict['body'] = self.genInputPage() - self.dict['title'] = 'Delete Phenotype Trait Input Page' - if status == 'check': - PublishFreeze_Name = fd.formdata.getvalue('PublishFreeze_Name') - traitID = fd.formdata.getvalue('traitID') - self.dict['body'] = self.checkInputPage(PublishFreeze_Name, traitID) - self.dict['title'] = 'Delete Phenotype Trait Check Input Page' - if status == 'delete': - PublishFreeze_Name = fd.formdata.getvalue('PublishFreeze_Name') - traitID = fd.formdata.getvalue('traitID') - self.dict['body'] = self.deleteResultPage(PublishFreeze_Name, traitID) - self.dict['title'] = 'Delete Phenotype Trait Result Page' - - - def genInputPage(self): - - crossMenu = HT.Select(name='PublishFreeze_Name', onChange='xchange()') - - self.cursor.execute('select PublishFreeze.Name from PublishFreeze, InbredSet where InbredSetId=InbredSet.Id') - result = self.cursor.fetchall() - - for one_row in result: - Name = one_row - crossMenu.append(tuple([Name,Name])) - - TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee') - - deletePhenotypeTraitForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='deletePhenotypeTraitForm', submit=HT.Input(type='hidden')) - deletePhenotypeTraitForm.append( - HT.Blockquote( - HT.Font('Publish Freeze Name '), - crossMenu, - HT.Font(' Phenotype Trait ID '), - HT.Input(type='text' ,name='traitID',value='', size=20,maxlength=20), - HT.Input(type='Submit', value='Submit', Class="button")), - HT.Input(type='hidden',name='FormID',value='deletePhenotypeTrait'), - HT.Input(type='hidden',name='ifVerified',value='GN@UTHSC'), - HT.Input(type='hidden',name='status',value='check') - ) - - TD_LR.append(deletePhenotypeTraitForm) - - return str(TD_LR) - - - def checkInputPage(self, PublishFreeze_Name, traitID): - TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee') - - try: - db = webqtlDataset(PublishFreeze_Name, self.cursor) - thisTrait = webqtlTrait(db=db, cursor=self.cursor, name=traitID) - thisTrait.retrieveInfo() - setDescription = thisTrait.genHTML(dispFromDatabase=1, privilege=self.privilege, userName=self.userName, authorized_users=thisTrait.authorized_users) - except: - TD_LR.append( HT.Font('This trait is not found. Please go back to check if you selected correct Group Name and inputed correct trait ID.', color='red') ) - return str(TD_LR) - - #TD_LR.append(HT.Font('Publish Freeze Name: %s' % PublishFreeze_Name, color='red'),HT.BR(), HT.Font('trait ID: %s' % traitID, color='red'), HT.BR()) - - formMain = HT.Form(cgi=os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='showDatabase', submit=HT.Input(type='hidden')) - - formMain.append( - HT.Blockquote( - HT.Font('The trait '), - setDescription, - HT.Font(' will be deleted.'), - HT.BR(), HT.BR(), - HT.Font('Please open the trait and make sure you do want to delete it.', color = 'red') - ), - HT.Input(type='hidden',name='FormID',value=''), - HT.Input(type='hidden',name='database',value=''), - HT.Input(type='hidden',name='ProbeSetID',value=''), - HT.Input(type='hidden',name='CellID',value='') - ) - - deletePhenotypeTraitForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='deletePhenotypeTraitForm', submit=HT.Input(type='hidden')) - deletePhenotypeTraitForm.append( - HT.Input(type='Submit', value='Delete Trait', Class="button"), - HT.Input(type='hidden',name='FormID',value='deletePhenotypeTrait'), - HT.Input(type='hidden',name='ifVerified',value='GN@UTHSC'), - HT.Input(type='hidden',name='status',value='delete'), - HT.Input(type='hidden',name='PublishFreeze_Name',value=db), - HT.Input(type='hidden',name='traitID',value=traitID) - ) - - - TD_LR.append(formMain, HT.BR(), HT.BR(), deletePhenotypeTraitForm) - return str(TD_LR) - - def deleteResultPage(self, PublishFreeze_Name, traitID): - TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee') - - #TD_LR.append(HT.Font('Publish Freeze Name: %s' % PublishFreeze_Name, color='red'),HT.BR(), HT.Font('trait ID: %s' % traitID, color='red'), HT.BR(), HT.BR(), 'Being constructed...') - - self.cursor.execute( 'select InbredSetId from PublishFreeze where Name="%s"' % PublishFreeze_Name ) - InbredSetId = self.cursor.fetchone()[0] - #TD_LR.append(HT.BR(), HT.BR(), 'InbredSetId: ', InbredSetId) - - self.cursor.execute( 'select PhenotypeId, PublicationId, DataId from PublishXRef where Id = %s and InbredSetId = %s' % (traitID, InbredSetId) ) - result = self.cursor.fetchone() - PhenotypeId, PublicationId, DataId = result - - #TD_LR.append(HT.BR(), 'PhenotypeId: ', PhenotypeId) - #TD_LR.append(HT.BR(), 'PublicationId: ', PublicationId) - #TD_LR.append(HT.BR(), 'DataId: ', DataId) - - #PublishData - self.cursor.execute('delete from PublishData where Id = %s' % DataId) - - #PublishSE - self.cursor.execute('delete from PublishSE where DataId = %s' % DataId) - - #NStrain - self.cursor.execute('delete from NStrain where DataId = %s' % DataId) - - #Phenotype - self.cursor.execute( 'select count(*) from PublishXRef where PhenotypeId = %s' % PhenotypeId ) - PhenotypeId_count = self.cursor.fetchone()[0] - #TD_LR.append(HT.BR(), HT.BR(), 'PhenotypeId_count: ', PhenotypeId_count) - if PhenotypeId_count > 1: - pass - else: - self.cursor.execute('delete from Phenotype where Id = %s' % PhenotypeId) - - #Publication - self.cursor.execute( 'select count(*) from PublishXRef where PublicationId = %s' % PublicationId ) - PublicationId_count = self.cursor.fetchone()[0] - #TD_LR.append(HT.BR(), 'PublicationId_count: ', PublicationId_count) - if PublicationId_count > 1: - pass - else: - self.cursor.execute('delete from Publication where Id = %s' % PublicationId) - - #PublishXRef - self.cursor.execute( 'delete from PublishXRef where Id = %s and InbredSetId = %s' % (traitID, InbredSetId) ) - - #TD_LR.append(HT.BR(), HT.BR() ) - TD_LR.append('The trait %s has been successfully deleted from %s' % (traitID, PublishFreeze_Name)) - - return str(TD_LR) diff --git a/web/webqtl/management/editHeaderFooter.py b/web/webqtl/management/editHeaderFooter.py deleted file mode 100755 index 1461fa3a..00000000 --- a/web/webqtl/management/editHeaderFooter.py +++ /dev/null @@ -1,200 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -from htmlgen import HTMLgen2 as HT -import os -import string -import urlparse - -from base.templatePage import templatePage -from base import webqtlConfig - -# 20100309 Lei Yan -class editHeaderFooter(templatePage): - - htmlPath = webqtlConfig.ChangableHtmlPath - - def __init__(self, fd): - - templatePage.__init__(self, fd) - - self.templateInclude = 1 - self.dict['title'] = "Editing HTML" - - if not self.updMysql(): - return - - path = fd.formdata.getvalue('path') - preview = fd.formdata.getvalue('preview') - newHtmlCode = fd.formdata.getvalue('htmlSrc') - hf = fd.formdata.getvalue('hf') - - if newHtmlCode: - newHtmlCode = string.replace(newHtmlCode,"&", "&") - if path and preview: - self.templateInclude = 0 - if hf=='h': - tempH = newHtmlCode - fp = open(self.htmlPath+'/footer.html', 'r') - tempF = fp.read() - fp.close() - else: - fp = open(self.htmlPath+'/header.html', 'r') - tempH = fp.read() - fp.close() - tempF = newHtmlCode - tempHtml = """ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> -<HTML><HEAD><TITLE>Header Footer Test</TITLE> -<META http-equiv=Content-Type content="text/html; charset=iso-8859-1"> -<LINK REL="stylesheet" TYPE="text/css" HREF='/css/general.css'> -<LINK REL="stylesheet" TYPE="text/css" HREF='/css/menu.css'> -<link rel="stylesheet" media="all" type="text/css" href="/css/tabbed_pages.css" /> -<SCRIPT SRC="/javascript/webqtl.js"></SCRIPT> -<SCRIPT SRC="/javascript/tooltip.js"></SCRIPT> -<SCRIPT SRC="/javascript/dhtml.js"></SCRIPT> -<SCRIPT SRC="/javascript/beta2.js"></SCRIPT> -<script src="/javascript/tabbed_pages.js" type="text/javascript"></script> -</HEAD> -<BODY bottommargin="2" leftmargin="2" rightmargin="2" topmargin="2" text=#000000 bgColor=#ffffff> -<TABLE cellSpacing=5 cellPadding=4 width="100%%" border=0> - <TBODY> - <TR> - %s - </TR> - <TR> - <TD bgColor=#eeeeee class="solidBorder"> - <Table width= "100%%" cellSpacing=0 cellPadding=5> - <TR> - <!-- split from Here --> - <!-- Body Start from Here --> - <br><br><br><br><br><br><br><br><br><br><br><br> - <center style="font-size:16px;font-family:verdana;color:red">Header Footer Test</center> - <br><br><br><br><br><br><br><br><br><br><br><br> - </TR></TABLE> - </TD> - </TR> - <TR> - <TD align=center bgColor=#ddddff class="solidBorder"> - <!--Start of footer--> - <TABLE width="100%%"> - %s - </TABLE> - <!--End of footer--> - </TD> - </TR> -</TABLE> -<!-- /Footer --> -<!-- menu script itself. you should not modify this file --> -<script language="JavaScript" src="/javascript/menu_new.js"></script> -<!-- items structure. menu hierarchy and links are stored there --> -<script language="JavaScript" src="/javascript/menu_items.js"></script> -<!-- files with geometry and styles structures --> -<script language="JavaScript" src="/javascript/menu_tpl.js"></script> -<script language="JavaScript"> - <!--// - // Note where menu initialization block is located in HTML document. - // Don't try to position menu locating menu initialization block in - // some table cell or other HTML element. Always put it before </body> - // each menu gets two parameters (see demo files) - // 1. items structure - // 2. geometry structure - new menu (MENU_ITEMS, MENU_POS); - // make sure files containing definitions for these variables are linked to the document - // if you got some javascript error like "MENU_POS is not defined", then you've made syntax - // error in menu_tpl.js file or that file isn't linked properly. - // also take a look at stylesheets loaded in header in order to set styles - //--> -</script> -</BODY> -</HTML> -""" %(tempH, tempF) - self.debug = tempHtml - elif path: - #edit result - fileName = self.htmlPath + path - - fp1 = open(fileName, 'w') - fp1.write(newHtmlCode) - fp1.close() - - fp1 = open(fileName, 'r') - lines = fp1.readlines() - fp1.close - - if 'h'==hf: - fp2 = open(self.htmlPath + '/javascript/header.js', 'w') - else: - fp2 = open(self.htmlPath + '/javascript/footer.js', 'w') - fp2.write("ctext = ''\r\n") - fp2.flush() - for line in lines: - fp2.write("ctext += '%s'\r\n" %(line.rstrip())) - fp2.flush() - fp2.write('document.write(ctext)') - fp2.flush() - fp2.close() - - TD_LR = HT.TD(valign="top",colspan=2,bgcolor="#eeeeee", height=200) - mainTitle = HT.Paragraph("Edit HTML", Class="title") - url = HT.Href(text = "page", url =path, Class = "normal") - intro = HT.Blockquote("This ",url, " has been succesfully modified. ") - TD_LR.append(mainTitle, intro) - self.dict['body'] = TD_LR - elif fd.refURL: - #retrieve file to be edited - #refURL = os.environ['HTTP_REFERER'] - addressing_scheme, network_location, path, parameters, query, fragment_identifier = urlparse.urlparse(fd.refURL) - if 'h'==hf: - path = "/header.html" - else: - path = "/footer.html" - fileName = self.htmlPath + path - fp = open(fileName,'r') - htmlCode = fp.read() - htmlCode = string.replace(htmlCode, "&","&") - fp.close() - form = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), name='editHtml',submit=HT.Input(type='hidden')) - inputBox = HT.Textarea(name='htmlSrc', cols="100", rows=30,text=htmlCode) - hddn = {'FormID':'editHeaderFooter', 'path':path, 'preview':'', 'hf':hf} - for key in hddn.keys(): - form.append(HT.Input(name=key, value=hddn[key], type='hidden')) - previewButton = HT.Input(type='button',name='previewhtml', value='Preview',Class="button", onClick= "editHTML(this.form, 'preview');") - submitButton = HT.Input(type='button',name='submitchange', value='Submit Change',Class="button", onClick= "editHTML(this.form, 'submit');") - resetButton = HT.Input(type='reset',Class="button") - form.append(HT.Center(inputBox, HT.P(), previewButton, submitButton, resetButton)) - TD_LR = HT.TD(valign="top",colspan=2,bgcolor="#eeeeee") - mainTitle = HT.Paragraph("Edit HTML", Class="title") - intro = HT.Blockquote("You may edit the HTML source code in the editbox below, or you can copy the content of the editbox to your favorite HTML editor. ") - imgUpload = HT.Href(url="javascript:openNewWin('/upload.html', 'menubar=0,toolbar=0,location=0,resizable=0,status=1,scrollbars=1,height=400, width=600');", text="here", Class="normalsize") - intro2 = HT.Blockquote("Click ", imgUpload, " to upload Images. ") - TD_LR.append(mainTitle, intro, intro2, HT.Center(form)) - self.dict['body'] = TD_LR - else: - heading = "Editing HTML" - detail = ["Error occured while trying to edit the html file."] - self.error(heading=heading,detail=detail,error="Error") - return diff --git a/web/webqtl/management/exportPhenotypeDatasetPage.py b/web/webqtl/management/exportPhenotypeDatasetPage.py deleted file mode 100755 index bbd86385..00000000 --- a/web/webqtl/management/exportPhenotypeDatasetPage.py +++ /dev/null @@ -1,228 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -import os -import string -import pyXLWriter as xl -import time - -import reaper -from htmlgen import HTMLgen2 as HT - -from base.templatePage import templatePage -from utility import webqtlUtil -from base import webqtlConfig -from base.webqtlTrait import webqtlTrait - - - -#XZ, 11/06/2009: Xiaodong created this class -class exportPhenotypeDatasetPage(templatePage): - - def __init__(self, fd): - - templatePage.__init__(self, fd) - - if not self.openMysql(): - return - - ifVerified = fd.formdata.getvalue('ifVerified') - status = fd.formdata.getvalue('status') - - if ifVerified != 'GN@UTHSC': - heading = "Error page" - detail = ["You are NoT verified as administrator."] - self.error(heading=heading,detail=detail) - return - else: - if status == 'input': - self.dict['body'] = self.genInputPage() - self.dict['title'] = 'Export Phenotype Dataset Input Page' - if status == 'output': - PublishFreeze_Name = fd.formdata.getvalue('PublishFreeze_Name') - self.dict['body'] = self.exportDatasetPage( fd, PublishFreeze_Name ) - self.dict['title'] = 'Export Phenotype Dataset Page' - - - def genInputPage(self): - - crossMenu = HT.Select(name='PublishFreeze_Name', onChange='xchange()') - - self.cursor.execute('select PublishFreeze.Name from PublishFreeze, InbredSet where InbredSetId=InbredSet.Id') - result = self.cursor.fetchall() - - for one_row in result: - Name = one_row - crossMenu.append(tuple([Name,Name])) - - TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee') - - exportPhenotypeDatasetForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='exportPhenotypeDatasetForm', submit=HT.Input(type='hidden')) - exportPhenotypeDatasetForm.append( - HT.Blockquote( - HT.Font('Publish Freeze Name '), - crossMenu, - HT.Input(type='Submit', value='Submit', Class="button")), - HT.Input(type='hidden',name='FormID',value='exportPhenotypeDataset'), - HT.Input(type='hidden',name='status',value='output'), - HT.Input(type='hidden',name='ifVerified',value='GN@UTHSC') - ) - - TD_LR.append( exportPhenotypeDatasetForm ) - - return str(TD_LR) - - - def exportDatasetPage(self, fd, PublishFreeze_Name): - - #return PublishFreeze_Name - - if not self.openMysql(): - return - - self.cursor.execute( "select InbredSet.Name from PublishFreeze, InbredSet where PublishFreeze.InbredSetId=InbredSet.Id and PublishFreeze.Name='%s'" % PublishFreeze_Name ) - self.RISet = self.cursor.fetchone()[0] - - fd.RISet = self.RISet - fd.incparentsf1 = 1 - fd.readGenotype() - strainlist = fd.f1list + fd.strainlist - - #return str(strainlist) - - self.cursor.execute("Select Species.Name from Species, InbredSet where InbredSet.SpeciesId = Species.Id and InbredSet.Name = '%s'" % fd.RISet) - self.Species = self.cursor.fetchone()[0] - - #return Species - - self.searchResult = [] - - self.cursor.execute("Select PublishXRef.Id from PublishXRef, InbredSet where PublishXRef.InbredSetId = InbredSet.Id and InbredSet.Name = '%s'" % self.RISet) - result = self.cursor.fetchall() - - for one_result in result: - self.searchResult.append( "%s::%s" % (PublishFreeze_Name, one_result[0]) ) - - #return self.searchResult - - - fields = ["ID", "Species", "Cross", "Database", "ProbeSetID / RecordID", "Symbol", "Description", "ProbeTarget", "PubMed_ID", "Phenotype", "Chr", "Mb", "Alias", "Gene_ID", "UniGene_ID", "Strand_Probe ", "Strand_Gene ", -"Probe_set_specificity", "Probe_set_BLAT_score", "Probe_set_BLAT_Mb_start", "Probe_set_BLAT_Mb_end ", "QTL_Chr", "Locus_at_Peak", "Max_LRS", "P_value_of_MAX", "Mean_Expression"] + strainlist - - - if self.searchResult: - traitList = [] - for item in self.searchResult: - thisTrait = webqtlTrait(fullname=item, cursor=self.cursor) - thisTrait.retrieveInfo(QTL=1) - thisTrait.retrieveData(strainlist=strainlist) - traitList.append(thisTrait) - - text = [fields] - for i, thisTrait in enumerate(traitList): - if thisTrait.db.type == 'ProbeSet': - if not thisTrait.cellid: #ProbeSet - text.append([str(i+1), self.Species, self.RISet, thisTrait.db.fullname, thisTrait.name, thisTrait.symbol, thisTrait.description, thisTrait.probe_target_description,"", "", thisTrait.chr, thisTrait.mb, thisTrait.alias, thisTrait.geneid, thisTrait.unigeneid, thisTrait.strand_probe, thisTrait.strand_gene, thisTrait.probe_set_specificity, thisTrait.probe_set_blat_score, thisTrait.probe_set_blat_mb_start, thisTrait.probe_set_blat_mb_end, locusChr[thisTrait.locus], thisTrait.locus, thisTrait.lrs, thisTrait.pvalue]) - else: #Probe - text.append([str(i+1), self.Species, self.RISet, thisTrait.db.fullname, thisTrait.name + " : " + thisTrait.cellid, thisTrait.symbol, thisTrait.description, thisTrait.probe_target_description,"", "", thisTrait.chr, thisTrait.mb, thisTrait.alias, thisTrait.geneid, thisTrait.unigeneid, "", "", "", "", "", "", "", "", "", ""]) - elif thisTrait.db.type == 'Publish': - if thisTrait.pre_publication_description: - if thisTrait.pubmed_id: - text.append([str(i+1), self.Species, self.RISet, thisTrait.db.fullname, thisTrait.name, "", "", "", thisTrait.pubmed_id, thisTrait.post_publication_description, "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""]) - else: - text.append([str(i+1), self.Species, self.RISet, thisTrait.db.fullname, thisTrait.name, "", "", "", "", thisTrait.pre_publication_description, "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""]) - else: - text.append([str(i+1), self.Species, self.RISet, thisTrait.db.fullname, thisTrait.name, "", "", "", thisTrait.pubmed_id, thisTrait.post_publication_description, "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""]) - - elif thisTrait.db.type == 'Temp': - text.append([str(i+1), self.Species, self.RISet, thisTrait.db.fullname, thisTrait.name, "", thisTrait.description, "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""]) - elif thisTrait.db.type == 'Geno': - text.append([str(i+1), self.Species, self.RISet, thisTrait.db.fullname, thisTrait.name, "", thisTrait.name,"", "", "", thisTrait.chr, thisTrait.mb, "", "", "", "", "", "", "", "", "", "", "", "", ""]) - else: - continue - - testval = thisTrait.exportData(strainlist) - try: - mean = reaper.anova(testval)[0] - except: - mean = 'N/A' - text[-1].append(mean) - text[-1] += testval - if len(text[0]) < 255 or len(text) < 255: - transpose = 0 - if len(text[0]) >= 255: - text = webqtlUtil.transpose(text) - transpose = 1 - filename = os.path.join(webqtlConfig.TMPDIR, webqtlUtil.generate_session() +'.xls') - - # Create a new Excel workbook - workbook = xl.Writer(filename) - worksheet = workbook.add_worksheet() - headingStyle = workbook.add_format(align = 'center', bold = 1, size=13, color = 'green') - titleStyle = workbook.add_format(align = 'left', bold = 0, size=13, border = 1, border_color="gray") - - ##Write title Info - worksheet.write([0, 0], "Data source: The GeneNetwork at %s" % webqtlConfig.PORTADDR, titleStyle) - worksheet.write([1, 0], "Citations: Please see %s/reference.html" % webqtlConfig.PORTADDR, titleStyle) - worksheet.write([2, 0], "Date : %s" % time.strftime("%B %d, %Y", time.gmtime()), titleStyle) - worksheet.write([3, 0], "Time : %s GMT" % time.strftime("%H:%M ", time.gmtime()), titleStyle) - worksheet.write([4, 0], "Status of data ownership: Possibly unpublished data; please see %s/statusandContact.html for details on sources, ownership, and usage of these data." % webqtlConfig.PORTADDR, titleStyle) - worksheet.write([6, 0], "This output file contains data from %d GeneNetwork databases listed below" % len(traitList), titleStyle) - - # Row and column are zero indexed - nrow = startRow = 8 - for row in text: - for ncol, cell in enumerate(row): - if nrow == startRow: - worksheet.write([nrow, ncol], cell.strip(), headingStyle) - worksheet.set_column([ncol, ncol], 2*len(cell)) - else: - worksheet.write([nrow, ncol], cell) - nrow += 1 - - worksheet.write([nrow+1, 0], "Funding for The GeneNetwork: NIAAA (U01AA13499, U24AA13513), NIDA, NIMH, and NIAAA (P20-DA 21131), NCI MMHCC (U01CA105417), and NCRR (U24 RR021760)", titleStyle) - worksheet.write([nrow+2, 0], "PLEASE RETAIN DATA SOURCE INFORMATION WHENEVER POSSIBLE", titleStyle) - workbook.close() - - fp = open(filename, 'rb') - text = fp.read() - fp.close() - - self.content_type = 'application/xls' - self.content_disposition = 'attachment; filename=%s' % ('export-%s.xls' % time.strftime("%y-%m-%d-%H-%M")) - self.attachment = text - else: - self.content_type = 'application/xls' - self.content_disposition = 'attachment; filename=%s' % ('export-%s.txt' % time.strftime("%y-%m-%d-%H-%M")) - for item in text: - self.attachment += string.join(map(str, item), '\t')+ "\n" - self.cursor.close() - else: - fd.req.content_type = 'text/html' - heading = 'Export Collection' - detail = [HT.Font('Error : ',color='red'),HT.Font('Error occurs while retrieving data from database.',color='black')] - self.error(heading=heading,detail=detail) - diff --git a/web/webqtl/management/managerMainPage.py b/web/webqtl/management/managerMainPage.py deleted file mode 100755 index 36f744ad..00000000 --- a/web/webqtl/management/managerMainPage.py +++ /dev/null @@ -1,130 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -import os - -from htmlgen import HTMLgen2 as HT - -from base.templatePage import templatePage -from utility import webqtlUtil -from base import webqtlConfig - -#XZ, 02/06/2009: Xiaodong created this class -class managerMainPage(templatePage): - - def __init__(self, fd): - - templatePage.__init__(self, fd) - - if not self.openMysql(): - return - - ifVerified = None - - ifVerified = fd.formdata.getvalue('ifVerified') - - if ifVerified != 'GN@UTHSC': - user = fd.formdata.getvalue('user') - password = fd.formdata.getvalue('password') - privilege, user_id, userExist = webqtlUtil.authUser(user,password,self.cursor,encrypt = None)[:3] - - if userExist and webqtlConfig.USERDICT[privilege] >= webqtlConfig.USERDICT['admin']: - ifVerified = True - - - if not ifVerified: - heading = "Error page" - detail = ["You do not have privilege to change system configuration."] - self.error(heading=heading,detail=detail) - return - else: - TD_LR = HT.TD(height=200,width="100%", bgColor='#eeeeee') - - heading = "Please click button to make your selection" - - createUserAccountForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='createUserAccountForm', submit=HT.Input(type='hidden')) - createUserAccountForm.append( - HT.Input(type='button', name='', value='Manage User Accounts', Class="button", onClick="submitToNewWindow(this.form);"), - HT.Input(type='hidden',name='FormID',value='createUserAccount'), - HT.Input(type='hidden',name='ifVerified',value='GN@UTHSC') - ) - - assignUserToDatasetForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='assignUserToDatasetForm', submit=HT.Input(type='hidden')) - assignUserToDatasetForm.append( - HT.Input(type='button', name='', value='Manage Confidential Datasets', Class="button", onClick="submitToNewWindow(this.form);"), - HT.Input(type='hidden',name='FormID',value='assignUserToDataset'), - HT.Input(type='hidden',name='ifVerified',value='GN@UTHSC') - ) - - deletePhenotypeTraitForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='deletePhenotypeTraitForm', submit=HT.Input(type='hidden')) - deletePhenotypeTraitForm.append( - HT.Input(type='button', name='', value='Delete Phenotype Trait', Class="button", onClick="submitToNewWindow(this.form);"), - HT.Input(type='hidden',name='FormID',value='deletePhenotypeTrait'), - HT.Input(type='hidden',name='ifVerified',value='GN@UTHSC'), - HT.Input(type='hidden',name='status',value='input') - ) - - exportPhenotypeDatasetForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='exportPhenotypeDatasetForm', submit=HT.Input(type='hidden')) - exportPhenotypeDatasetForm.append( - HT.Input(type='button', name='', value='Export Phenotype Dataset', Class="button", onClick="submitToNewWindow(this.form);"), - HT.Input(type='hidden',name='FormID',value='exportPhenotypeDataset'), - HT.Input(type='hidden',name='ifVerified',value='GN@UTHSC'), - HT.Input(type='hidden',name='status',value='input') - ) - - updateGenotypeForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='updateGenotypeForm', submit=HT.Input(type='hidden')) - updateGenotypeForm.append( - HT.Input(type='button', name='', value='Update Genotype', Class="button", onClick="submitToNewWindow(this.form);"), - HT.Input(type='hidden',name='FormID',value='updGeno'), - HT.Input(type='hidden',name='ifVerified',value='GN@UTHSC') - ) - - editHeaderForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='editHeaderForm', submit=HT.Input(type='hidden')) - editHeaderForm.append( - HT.Input(type='button', name='', value='Edit Header', Class="button", onClick="submitToNewWindow(this.form);"), - HT.Input(type='hidden', name='FormID', value='editHeaderFooter'), - HT.Input(type='hidden', name='hf', value='h'), - ) - - editFooterForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='editFooterForm', submit=HT.Input(type='hidden')) - editFooterForm.append( - HT.Input(type='button', name='', value='Edit Footer', Class="button", onClick="submitToNewWindow(this.form);"), - HT.Input(type='hidden', name='FormID', value='editHeaderFooter'), - HT.Input(type='hidden', name='hf', value='f'), - ) - - TD_LR.append(heading, HT.P(),HT.P(), - createUserAccountForm, HT.P(),HT.P(), - assignUserToDatasetForm, HT.P(),HT.P(), - deletePhenotypeTraitForm, HT.P(),HT.P(), - exportPhenotypeDatasetForm, HT.P(),HT.P(), - updateGenotypeForm, HT.P(),HT.P(), - editHeaderForm, HT.P(),HT.P(), - editFooterForm) - - self.dict['body'] = str(TD_LR) - self.dict['title'] = 'Manager Main Page' - |